Structure and regulation of the chromatin remodeller ISWI

Abstract

ISWI is a member of the SWI2/SNF2 family of chromatin remodellers, which also includes Snf2, Chd1, and Ino80. ISWI is the catalytic subunit of several chromatin remodelling complexes, which mobilize nucleosomes along genomic DNA, promoting replication progression, transcription repression, heterochromatin formation, and many other nuclear processes. The ATPase motor of ISWI is an autonomous remodelling machine, whereas its carboxy (C)-terminal HAND-SAND-SLIDE (HSS) domain functions in binding extranucleosomal linker DNA. The activity of the catalytic core of ISWI is inhibited by the regulatory AutoN and NegC domains, which are in turn antagonized by the H4 tail and extranucleosomal DNA, respectively, to ensure the appropriate chromatin landscape in cells. How AutoN and NegC inhibit ISWI and regulate its nucleosome-centring activity remains elusive. Here we report the crystal structures of ISWI from the thermophilic yeast Myceliophthora thermophila and its complex with a histone H4 peptide. Our data show the amino (N)-terminal AutoN domain contains two inhibitory elements, which collectively bind the second RecA-like domain (core2), holding the enzyme in an inactive conformation. The H4 peptide binds to the core2 domain coincident with one of the AutoN-binding sites, explaining the ISWI activation by H4. The H4-binding surface is conserved in Snf2 and functions beyond AutoN regulation. The C-terminal NegC domain is involved in binding to the core2 domain and functions as an allosteric element for ISWI to respond to the extranucleosomal DNA length.

Electron cryo-microscopy structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome

“…Similar to observations for the Swi2/Snf2 ATPase domain and Chd1, our structure implies a large conformational rearrangement in the RecA lobes of SNF2h upon nucleosome binding (Farnung et al, 2017; Hauk et al, 2010; Liu et al, 2017; Sundaramoorthy et al, 2018; 2017; Xia et al, 2016; Yan et al, 2016) (Figure 3B, Figure 3-supplement 2). A large conformational change is also implied for the brace helix extending from lobe 2 (Figure 3-supplement 3A, orange helices) (Liu et al, 2017; Yan et al, 2016).…”

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

“…This is indeed the case as the chromodomains undergo an 18 degree rotation when compared to the orientation observed in The repositioning of ATPase lobe II enables contacts to be made with nucleosomal DNA (see below), the histone H4 tail and the histone H3 alpha 1 helix ( Figure 2 -figure supplement 4).These are the only direct contacts with histone components of the nucleosome. The contact with the H4 tails is conserved in mtISWI and Snf2 (Liu et al, 2017;Yan et al, 2016). The conservation of this contact in Chd1 enzymes is consistent with the H4 tail playing an important role in regulating Chd1 activity; deletion or mutation of the H4 tail has been shown to reduce nucleosome sliding and ATPase activity (Ferreira et al, 2007).…”

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

“…These are the only direct contacts with histone components of the nucleosome. The contact with the H4 tails is conserved in mtISWI and Snf2 (Liu et al, 2017; Yan et al, 2016). D729 and E669 are conserved across all classes of remodelling enzyme but D725 is not as well conserved in Snf2-related enzymes (Figure 2—figure supplement 4B).…”